broad.pda.seq.protection.TwoSampleScanSkellamPeakCaller Class Reference

Collaboration diagram for broad.pda.seq.protection.TwoSampleScanSkellamPeakCaller:

Public Member Functions
Collection< Annotation >	filterWindows (Collection< Annotation > windows) throws IOException
void	writeResults (Collection< Annotation > windows, String out) throws IOException
void	writeResult (Collection< Annotation > windows, FileWriter writer) throws IOException

Static Public Member Functions
static double	getPoissonLambda (int regionLength, double d, int windowSize)

Static Public Attributes
static double	EXPRESSION_PVALUE_CUTOFF = 0.01

Protected Member Functions
Annotation	trimPeak (Gene window) throws IOException

Static Protected Member Functions
static double	getSkellamPvalue (double backgroundLambda, double signalLambda, int backgroundCount, int signalCount) throws IOException

Protected Attributes
Map< String, Map< Gene, Double > >	backgroundScanPvalues
ScanStatisticDataAlignmentModel	backgroundData
String	backgroundName
TranscriptomeSpaceAlignmentModel	signalData
String	signalName
Map< String, Collection< Gene > >	genes
int	windowSize
int	stepSize
double	pValueCutoffSkellam
double	pValueCutoffScan
double	trimPeakByQuantile
TranscriptomeSpace	transcriptomeSpace
WindowProcessor< CountScore >	backgroundProcessor
WindowProcessor < ScanStatisticScore >	signalProcessor

Static Protected Attributes
static int	MIN_WINDOW_COUNT = 10
static Logger	logger = Logger.getLogger(TwoSampleScanSkellamPeakCaller.class.getName())

Detailed Description

Author

prussell

Member Function Documentation

Collection<Annotation> broad.pda.seq.protection.TwoSampleScanSkellamPeakCaller.filterWindows

(

Collection< Annotation >

windows

)

throws IOException

static double broad.pda.seq.protection.TwoSampleScanSkellamPeakCaller.getPoissonLambda ( int  regionLength, double  d, int  windowSize  )

static

Given a total number of reads, a region length, and a window size, get the parameter of the Poisson distribution modeling the number of reads in a window of this size

Parameters

regionLength	The total region length
d	The number of reads
windowSize	The window size

Returns

Lambda, the expected number of reads in the window under the null Poisson model

static double broad.pda.seq.protection.TwoSampleScanSkellamPeakCaller.getSkellamPvalue ( double  backgroundLambda, double  signalLambda, int  backgroundCount, int  signalCount  ) throws IOException

staticprotected

Compute Skellam P-value of read counts in a region given the two parameters

Parameters

backgroundLambda	Poisson lambda for background sample
signalLambda	Poisson lambda for signal sample
backgroundCount	The count for background sample
signalCount	The count for signal sample

Returns

The probability under the null hypothesis of observing a greater difference

Exceptions

IOException

Annotation broad.pda.seq.protection.TwoSampleScanSkellamPeakCaller.trimPeak ( Gene  window ) throws IOException

protected

Trim the peak to max contiguous subsequence of counts above a certain quantile

Parameters

window

The peak region

Returns

The trimmed peak

Exceptions

IOException

void broad.pda.seq.protection.TwoSampleScanSkellamPeakCaller.writeResult	(	Collection< Annotation >	windows,
		FileWriter	writer
	)		throws IOException

void broad.pda.seq.protection.TwoSampleScanSkellamPeakCaller.writeResults	(	Collection< Annotation >	windows,
		String	out
	)		throws IOException

Member Data Documentation

ScanStatisticDataAlignmentModel broad.pda.seq.protection.TwoSampleScanSkellamPeakCaller.backgroundData

protected

String broad.pda.seq.protection.TwoSampleScanSkellamPeakCaller.backgroundName

protected

WindowProcessor<CountScore> broad.pda.seq.protection.TwoSampleScanSkellamPeakCaller.backgroundProcessor

protected

Map<String, Map<Gene, Double> > broad.pda.seq.protection.TwoSampleScanSkellamPeakCaller.backgroundScanPvalues

protected

double broad.pda.seq.protection.TwoSampleScanSkellamPeakCaller.EXPRESSION_PVALUE_CUTOFF = 0.01

static

Transcriptome wide scan P value cutoff for expression of gene

Map<String, Collection<Gene> > broad.pda.seq.protection.TwoSampleScanSkellamPeakCaller.genes

protected

Logger broad.pda.seq.protection.TwoSampleScanSkellamPeakCaller.logger = Logger.getLogger(TwoSampleScanSkellamPeakCaller.class.getName())

staticprotected

int broad.pda.seq.protection.TwoSampleScanSkellamPeakCaller.MIN_WINDOW_COUNT = 10

staticprotected

double broad.pda.seq.protection.TwoSampleScanSkellamPeakCaller.pValueCutoffScan

protected

double broad.pda.seq.protection.TwoSampleScanSkellamPeakCaller.pValueCutoffSkellam

protected

TranscriptomeSpaceAlignmentModel broad.pda.seq.protection.TwoSampleScanSkellamPeakCaller.signalData

protected

String broad.pda.seq.protection.TwoSampleScanSkellamPeakCaller.signalName

protected

WindowProcessor<ScanStatisticScore> broad.pda.seq.protection.TwoSampleScanSkellamPeakCaller.signalProcessor

protected

int broad.pda.seq.protection.TwoSampleScanSkellamPeakCaller.stepSize

protected

TranscriptomeSpace broad.pda.seq.protection.TwoSampleScanSkellamPeakCaller.transcriptomeSpace

protected

double broad.pda.seq.protection.TwoSampleScanSkellamPeakCaller.trimPeakByQuantile

protected

int broad.pda.seq.protection.TwoSampleScanSkellamPeakCaller.windowSize

protected

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The documentation for this class was generated from the following file:

• java/broad/pda/seq/protection/TwoSampleScanSkellamPeakCaller.java